Starting phenix.real_space_refine on Wed Feb 4 20:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.map" model { file = "/net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9luv_63406/02_2026/9luv_63406.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 56 5.16 5 C 8064 2.51 5 N 2120 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12686 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6089 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Chain: "B" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6089 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.87, per 1000 atoms: 0.23 Number of scatterers: 12686 At special positions: 0 Unit cell: (98.77, 130.31, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 4 15.00 O 2442 8.00 N 2120 7.00 C 8064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 901 " - " ASN A 679 " " NAG A 902 " - " ASN A 413 " " NAG A 903 " - " ASN A 534 " " NAG B 901 " - " ASN B 679 " " NAG B 902 " - " ASN B 413 " " NAG B 903 " - " ASN B 534 " " NAG E 1 " - " ASN A 523 " " NAG F 1 " - " ASN A 69 " " NAG G 1 " - " ASN A 215 " " NAG H 1 " - " ASN A 361 " " NAG I 1 " - " ASN A 590 " " NAG J 1 " - " ASN B 523 " " NAG K 1 " - " ASN B 69 " " NAG L 1 " - " ASN B 215 " " NAG M 1 " - " ASN B 361 " " NAG N 1 " - " ASN B 590 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 432.9 milliseconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 16.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.593A pdb=" N PHE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.807A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.532A pdb=" N HIS A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.502A pdb=" N PHE A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 367 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 414 through 420 removed outlier: 4.100A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.772A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.776A pdb=" N ASN A 594 " --> pdb=" O PHE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.163A pdb=" N LEU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 removed outlier: 3.788A pdb=" N ARG A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 768 through 774 removed outlier: 4.068A pdb=" N ASN A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.664A pdb=" N GLN A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.680A pdb=" N HIS A 820 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 821 " --> pdb=" O GLY A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.592A pdb=" N PHE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.807A pdb=" N GLY B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.532A pdb=" N HIS B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.502A pdb=" N PHE B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 367 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 414 through 420 removed outlier: 4.100A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.772A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.776A pdb=" N ASN B 594 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.162A pdb=" N LEU B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.788A pdb=" N ARG B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 768 through 774 removed outlier: 4.067A pdb=" N ASN B 774 " --> pdb=" O ASN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 799 removed outlier: 3.664A pdb=" N GLN B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.681A pdb=" N HIS B 820 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 821 " --> pdb=" O GLY B 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 817 through 821' Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.499A pdb=" N VAL A 47 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR A 71 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 49 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 209 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 375 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 359 removed outlier: 6.778A pdb=" N ALA A 358 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 411 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.536A pdb=" N GLN A 531 " --> pdb=" O ARG A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 729 removed outlier: 7.229A pdb=" N LEU A 728 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 752 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 779 " --> pdb=" O LEU A 752 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.499A pdb=" N VAL B 47 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR B 71 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 49 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 209 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 375 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 359 removed outlier: 6.778A pdb=" N ALA B 358 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 411 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 530 through 531 removed outlier: 3.537A pdb=" N GLN B 531 " --> pdb=" O ARG B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 729 removed outlier: 7.230A pdb=" N LEU B 728 " --> pdb=" O ASP B 753 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 752 " --> pdb=" O MET B 777 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 779 " --> pdb=" O LEU B 752 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 142 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3995 1.34 - 1.46: 2047 1.46 - 1.58: 6820 1.58 - 1.69: 8 1.69 - 1.81: 76 Bond restraints: 12946 Sorted by residual: bond pdb=" CA ILE A 313 " pdb=" CB ILE A 313 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.50e-01 bond pdb=" C SER B 391 " pdb=" N PRO B 392 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.07e-01 bond pdb=" C SER A 391 " pdb=" N PRO A 392 " ideal model delta sigma weight residual 1.335 1.341 -0.007 1.28e-02 6.10e+03 2.88e-01 bond pdb=" CA SER A 391 " pdb=" C SER A 391 " ideal model delta sigma weight residual 1.522 1.528 -0.006 1.26e-02 6.30e+03 2.53e-01 bond pdb=" CA SER B 391 " pdb=" C SER B 391 " ideal model delta sigma weight residual 1.522 1.528 -0.006 1.26e-02 6.30e+03 2.34e-01 ... (remaining 12941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 17327 1.08 - 2.17: 160 2.17 - 3.25: 61 3.25 - 4.34: 8 4.34 - 5.42: 6 Bond angle restraints: 17562 Sorted by residual: angle pdb=" N VAL B 430 " pdb=" CA VAL B 430 " pdb=" C VAL B 430 " ideal model delta sigma weight residual 109.34 113.77 -4.43 2.08e+00 2.31e-01 4.54e+00 angle pdb=" N VAL A 430 " pdb=" CA VAL A 430 " pdb=" C VAL A 430 " ideal model delta sigma weight residual 109.34 113.73 -4.39 2.08e+00 2.31e-01 4.46e+00 angle pdb=" C SER A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta sigma weight residual 121.97 125.47 -3.50 1.80e+00 3.09e-01 3.78e+00 angle pdb=" C SER B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta sigma weight residual 121.97 125.45 -3.48 1.80e+00 3.09e-01 3.73e+00 angle pdb=" C TYR A 380 " pdb=" N VAL A 381 " pdb=" CA VAL A 381 " ideal model delta sigma weight residual 121.97 125.29 -3.32 1.80e+00 3.09e-01 3.40e+00 ... (remaining 17557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8002 34.82 - 69.64: 264 69.64 - 104.46: 22 104.46 - 139.28: 0 139.28 - 174.10: 2 Dihedral angle restraints: 8290 sinusoidal: 3816 harmonic: 4474 Sorted by residual: dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual 93.00 170.55 -77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 170.54 -77.54 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" O4' C D 3 " pdb=" C1' C D 3 " pdb=" N1 C D 3 " pdb=" C2 C D 3 " ideal model delta sinusoidal sigma weight residual -128.00 46.10 -174.10 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 8287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1256 0.027 - 0.054: 591 0.054 - 0.081: 124 0.081 - 0.107: 84 0.107 - 0.134: 57 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA VAL A 219 " pdb=" N VAL A 219 " pdb=" C VAL A 219 " pdb=" CB VAL A 219 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 69 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2109 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 112 " -0.013 5.00e-02 4.00e+02 1.93e-02 5.93e-01 pdb=" N PRO B 113 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 112 " -0.013 5.00e-02 4.00e+02 1.92e-02 5.92e-01 pdb=" N PRO A 113 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 434 " 0.012 5.00e-02 4.00e+02 1.81e-02 5.21e-01 pdb=" N PRO A 435 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.010 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1904 2.76 - 3.30: 11316 3.30 - 3.83: 21023 3.83 - 4.37: 24968 4.37 - 4.90: 42847 Nonbonded interactions: 102058 Sorted by model distance: nonbonded pdb=" OG1 THR A 788 " pdb=" OD1 ASP A 790 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 788 " pdb=" OD1 ASP B 790 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP B 572 " pdb=" OG SER B 574 " model vdw 2.355 3.040 nonbonded pdb=" OD1 ASP A 572 " pdb=" OG SER A 574 " model vdw 2.356 3.040 nonbonded pdb=" O LEU B 179 " pdb=" ND2 ASN B 214 " model vdw 2.367 3.120 ... (remaining 102053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 12990 Z= 0.061 Angle : 0.364 5.422 17678 Z= 0.194 Chirality : 0.039 0.134 2112 Planarity : 0.002 0.019 2182 Dihedral : 15.796 174.103 5314 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.28 % Allowed : 22.64 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.23), residues: 1498 helix: -2.82 (0.36), residues: 126 sheet: -0.80 (0.37), residues: 276 loop : 0.17 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 378 TYR 0.008 0.001 TYR B 184 PHE 0.007 0.001 PHE A 507 TRP 0.002 0.000 TRP A 796 HIS 0.006 0.000 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00110 (12946) covalent geometry : angle 0.35986 (17562) SS BOND : bond 0.00069 ( 16) SS BOND : angle 0.16904 ( 32) hydrogen bonds : bond 0.31595 ( 142) hydrogen bonds : angle 7.43576 ( 294) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.04575 ( 36) link_NAG-ASN : bond 0.00187 ( 16) link_NAG-ASN : angle 0.73835 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 VAL cc_start: 0.7978 (t) cc_final: 0.7549 (p) REVERT: A 276 ASN cc_start: 0.9285 (m-40) cc_final: 0.8539 (p0) REVERT: A 557 LEU cc_start: 0.9065 (mp) cc_final: 0.8824 (mm) REVERT: A 648 ASN cc_start: 0.8825 (m-40) cc_final: 0.8505 (m-40) REVERT: A 716 GLU cc_start: 0.8938 (tp30) cc_final: 0.8687 (tp30) REVERT: A 725 LEU cc_start: 0.9378 (tp) cc_final: 0.9142 (tm) REVERT: A 740 LYS cc_start: 0.9154 (ptmm) cc_final: 0.8846 (ptmm) REVERT: A 745 ASP cc_start: 0.8404 (m-30) cc_final: 0.8203 (m-30) REVERT: A 761 MET cc_start: 0.8525 (ppp) cc_final: 0.7787 (tmt) REVERT: A 797 TRP cc_start: 0.9116 (t60) cc_final: 0.8675 (t60) REVERT: B 191 VAL cc_start: 0.8017 (t) cc_final: 0.7579 (p) REVERT: B 551 ASN cc_start: 0.9322 (m110) cc_final: 0.8962 (m-40) REVERT: B 557 LEU cc_start: 0.9057 (mp) cc_final: 0.8815 (mm) REVERT: B 648 ASN cc_start: 0.8830 (m-40) cc_final: 0.8511 (m-40) REVERT: B 716 GLU cc_start: 0.8913 (tp30) cc_final: 0.8641 (tp30) REVERT: B 725 LEU cc_start: 0.9380 (tp) cc_final: 0.9132 (tm) REVERT: B 740 LYS cc_start: 0.9179 (ptmm) cc_final: 0.8884 (ptmm) REVERT: B 761 MET cc_start: 0.8560 (ppp) cc_final: 0.7791 (tmt) REVERT: B 785 PHE cc_start: 0.6069 (t80) cc_final: 0.5853 (t80) REVERT: B 797 TRP cc_start: 0.9130 (t60) cc_final: 0.8784 (t60) outliers start: 4 outliers final: 4 residues processed: 210 average time/residue: 0.6415 time to fit residues: 145.3878 Evaluate side-chains 81 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.0060 overall best weight: 1.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 323 GLN A 763 GLN B 137 ASN B 763 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068578 restraints weight = 25995.791| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.37 r_work: 0.2926 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12990 Z= 0.180 Angle : 0.568 8.181 17678 Z= 0.289 Chirality : 0.044 0.159 2112 Planarity : 0.004 0.044 2182 Dihedral : 7.437 175.598 2258 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 2.88 % Allowed : 24.61 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1498 helix: -3.37 (0.28), residues: 150 sheet: -1.08 (0.36), residues: 280 loop : 0.44 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 622 TYR 0.012 0.001 TYR A 751 PHE 0.028 0.002 PHE B 794 TRP 0.022 0.003 TRP B 793 HIS 0.006 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00416 (12946) covalent geometry : angle 0.56204 (17562) SS BOND : bond 0.00475 ( 16) SS BOND : angle 0.65749 ( 32) hydrogen bonds : bond 0.04816 ( 142) hydrogen bonds : angle 5.28084 ( 294) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 1.36204 ( 36) link_NAG-ASN : bond 0.00214 ( 16) link_NAG-ASN : angle 1.23217 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8562 (tp) cc_final: 0.8164 (pp) REVERT: A 291 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: A 557 LEU cc_start: 0.9146 (mp) cc_final: 0.8898 (mm) REVERT: A 648 ASN cc_start: 0.8901 (m-40) cc_final: 0.8476 (m-40) REVERT: A 716 GLU cc_start: 0.8918 (tp30) cc_final: 0.8658 (tp30) REVERT: A 740 LYS cc_start: 0.8979 (ptmm) cc_final: 0.8728 (ptmm) REVERT: A 742 PHE cc_start: 0.9187 (t80) cc_final: 0.8762 (t80) REVERT: A 761 MET cc_start: 0.8399 (ppp) cc_final: 0.7276 (ppp) REVERT: A 769 GLU cc_start: 0.8814 (tp30) cc_final: 0.8345 (tp30) REVERT: A 773 ASN cc_start: 0.9454 (m-40) cc_final: 0.8825 (m-40) REVERT: A 777 MET cc_start: 0.7683 (tpp) cc_final: 0.6898 (tpp) REVERT: A 778 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6712 (tt) REVERT: B 80 ILE cc_start: 0.8557 (tp) cc_final: 0.8140 (pp) REVERT: B 242 GLU cc_start: 0.8902 (pm20) cc_final: 0.8587 (pp20) REVERT: B 291 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: B 488 GLN cc_start: 0.7832 (pm20) cc_final: 0.7508 (tp40) REVERT: B 557 LEU cc_start: 0.9134 (mp) cc_final: 0.8884 (mm) REVERT: B 648 ASN cc_start: 0.8908 (m-40) cc_final: 0.8485 (m-40) REVERT: B 716 GLU cc_start: 0.8923 (tp30) cc_final: 0.8650 (tp30) REVERT: B 740 LYS cc_start: 0.8986 (ptmm) cc_final: 0.8730 (ptmm) REVERT: B 742 PHE cc_start: 0.9140 (t80) cc_final: 0.8754 (t80) REVERT: B 761 MET cc_start: 0.8582 (ppp) cc_final: 0.7750 (pp-130) REVERT: B 769 GLU cc_start: 0.8818 (tp30) cc_final: 0.8329 (tp30) REVERT: B 773 ASN cc_start: 0.9467 (m-40) cc_final: 0.8873 (m-40) REVERT: B 777 MET cc_start: 0.7689 (tpp) cc_final: 0.6911 (tpp) REVERT: B 778 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6828 (tt) outliers start: 41 outliers final: 16 residues processed: 139 average time/residue: 0.4279 time to fit residues: 66.4694 Evaluate side-chains 108 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 0.0980 chunk 148 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 298 HIS A 323 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 298 HIS ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.065471 restraints weight = 26385.025| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.37 r_work: 0.2850 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12990 Z= 0.175 Angle : 0.535 10.701 17678 Z= 0.276 Chirality : 0.043 0.140 2112 Planarity : 0.003 0.046 2182 Dihedral : 7.486 176.508 2256 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.54 % Favored : 95.19 % Rotamer: Outliers : 4.08 % Allowed : 23.28 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1498 helix: -3.34 (0.29), residues: 162 sheet: -1.22 (0.36), residues: 280 loop : 0.33 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.009 0.001 TYR A 233 PHE 0.027 0.002 PHE A 785 TRP 0.021 0.002 TRP A 796 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00410 (12946) covalent geometry : angle 0.53046 (17562) SS BOND : bond 0.00349 ( 16) SS BOND : angle 0.38579 ( 32) hydrogen bonds : bond 0.04581 ( 142) hydrogen bonds : angle 5.11264 ( 294) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.33489 ( 36) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 0.99769 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 98 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: A 416 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8824 (ptt) REVERT: A 557 LEU cc_start: 0.9232 (mp) cc_final: 0.8988 (mm) REVERT: A 648 ASN cc_start: 0.8968 (m-40) cc_final: 0.8530 (m-40) REVERT: A 716 GLU cc_start: 0.8933 (tp30) cc_final: 0.8607 (tp30) REVERT: A 742 PHE cc_start: 0.9286 (t80) cc_final: 0.8812 (t80) REVERT: A 743 LEU cc_start: 0.9492 (mt) cc_final: 0.9199 (mt) REVERT: A 745 ASP cc_start: 0.8860 (m-30) cc_final: 0.8658 (m-30) REVERT: A 761 MET cc_start: 0.7867 (ppp) cc_final: 0.7397 (ppp) REVERT: A 762 ILE cc_start: 0.8434 (pp) cc_final: 0.8210 (pp) REVERT: A 769 GLU cc_start: 0.8690 (tp30) cc_final: 0.8303 (tp30) REVERT: A 773 ASN cc_start: 0.9161 (m-40) cc_final: 0.8681 (m-40) REVERT: A 777 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: A 778 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7172 (tt) REVERT: B 291 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: B 416 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8824 (ptt) REVERT: B 557 LEU cc_start: 0.9231 (mp) cc_final: 0.8986 (mm) REVERT: B 648 ASN cc_start: 0.8975 (m-40) cc_final: 0.8544 (m-40) REVERT: B 716 GLU cc_start: 0.8912 (tp30) cc_final: 0.8604 (tp30) REVERT: B 742 PHE cc_start: 0.9257 (t80) cc_final: 0.8834 (t80) REVERT: B 761 MET cc_start: 0.8390 (ppp) cc_final: 0.7848 (ppp) REVERT: B 769 GLU cc_start: 0.8701 (tp30) cc_final: 0.8336 (tp30) REVERT: B 773 ASN cc_start: 0.9283 (m-40) cc_final: 0.8755 (m-40) REVERT: B 777 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6928 (tpp) REVERT: B 778 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7215 (tt) REVERT: B 796 TRP cc_start: 0.9001 (t60) cc_final: 0.8300 (t60) outliers start: 58 outliers final: 20 residues processed: 146 average time/residue: 0.3971 time to fit residues: 65.7436 Evaluate side-chains 111 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 298 HIS A 300 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS B 137 ASN B 298 HIS B 300 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.091695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060666 restraints weight = 26626.712| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.33 r_work: 0.2748 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 12990 Z= 0.324 Angle : 0.659 8.732 17678 Z= 0.336 Chirality : 0.048 0.129 2112 Planarity : 0.004 0.049 2182 Dihedral : 7.945 176.848 2254 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.94 % Favored : 93.79 % Rotamer: Outliers : 4.22 % Allowed : 23.07 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1498 helix: -3.53 (0.26), residues: 174 sheet: -1.51 (0.34), residues: 280 loop : 0.09 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 121 TYR 0.016 0.002 TYR B 751 PHE 0.028 0.002 PHE A 477 TRP 0.020 0.002 TRP A 796 HIS 0.007 0.001 HIS B 800 Details of bonding type rmsd covalent geometry : bond 0.00755 (12946) covalent geometry : angle 0.65110 (17562) SS BOND : bond 0.00545 ( 16) SS BOND : angle 0.58456 ( 32) hydrogen bonds : bond 0.04979 ( 142) hydrogen bonds : angle 5.13142 ( 294) link_BETA1-4 : bond 0.00286 ( 12) link_BETA1-4 : angle 1.80092 ( 36) link_NAG-ASN : bond 0.00579 ( 16) link_NAG-ASN : angle 1.49313 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 90 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8587 (tp) cc_final: 0.8071 (pp) REVERT: A 291 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: A 360 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8481 (tpp) REVERT: A 517 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 557 LEU cc_start: 0.9337 (mp) cc_final: 0.9133 (mm) REVERT: A 673 MET cc_start: 0.9169 (mmt) cc_final: 0.8881 (mmt) REVERT: A 716 GLU cc_start: 0.8910 (tp30) cc_final: 0.8569 (tp30) REVERT: A 761 MET cc_start: 0.8210 (ppp) cc_final: 0.7536 (ppp) REVERT: A 769 GLU cc_start: 0.8717 (tp30) cc_final: 0.8413 (tp30) REVERT: A 773 ASN cc_start: 0.9261 (m-40) cc_final: 0.8673 (m-40) REVERT: B 80 ILE cc_start: 0.8597 (tp) cc_final: 0.8066 (pp) REVERT: B 291 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: B 517 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 557 LEU cc_start: 0.9331 (mp) cc_final: 0.9129 (mm) REVERT: B 673 MET cc_start: 0.9173 (mmt) cc_final: 0.8882 (mmt) REVERT: B 716 GLU cc_start: 0.8910 (tp30) cc_final: 0.8580 (tp30) REVERT: B 761 MET cc_start: 0.8428 (ppp) cc_final: 0.7840 (ppp) REVERT: B 769 GLU cc_start: 0.8749 (tp30) cc_final: 0.8520 (tp30) REVERT: B 773 ASN cc_start: 0.9211 (m-40) cc_final: 0.8751 (m-40) REVERT: B 797 TRP cc_start: 0.9132 (t-100) cc_final: 0.8916 (t-100) outliers start: 60 outliers final: 19 residues processed: 141 average time/residue: 0.4177 time to fit residues: 65.6844 Evaluate side-chains 98 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 298 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 298 HIS ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.095399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064413 restraints weight = 26281.995| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.36 r_work: 0.2837 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12990 Z= 0.096 Angle : 0.520 8.365 17678 Z= 0.267 Chirality : 0.042 0.152 2112 Planarity : 0.003 0.045 2182 Dihedral : 7.678 177.073 2254 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.67 % Favored : 95.06 % Rotamer: Outliers : 2.60 % Allowed : 25.67 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1498 helix: -3.40 (0.28), residues: 174 sheet: -1.61 (0.34), residues: 284 loop : 0.13 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 121 TYR 0.010 0.001 TYR B 185 PHE 0.024 0.001 PHE B 747 TRP 0.022 0.002 TRP A 796 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00218 (12946) covalent geometry : angle 0.51606 (17562) SS BOND : bond 0.00190 ( 16) SS BOND : angle 0.30703 ( 32) hydrogen bonds : bond 0.03567 ( 142) hydrogen bonds : angle 4.81360 ( 294) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 1.21412 ( 36) link_NAG-ASN : bond 0.00194 ( 16) link_NAG-ASN : angle 0.89288 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8576 (tp) cc_final: 0.8080 (pp) REVERT: A 291 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: A 557 LEU cc_start: 0.9303 (mp) cc_final: 0.9087 (mm) REVERT: A 716 GLU cc_start: 0.8906 (tp30) cc_final: 0.8572 (tp30) REVERT: A 742 PHE cc_start: 0.9355 (t80) cc_final: 0.9023 (t80) REVERT: A 769 GLU cc_start: 0.8759 (tp30) cc_final: 0.8374 (tp30) REVERT: A 773 ASN cc_start: 0.9256 (m-40) cc_final: 0.8576 (m-40) REVERT: A 807 TYR cc_start: 0.9404 (m-80) cc_final: 0.9134 (m-80) REVERT: B 80 ILE cc_start: 0.8566 (tp) cc_final: 0.8045 (pp) REVERT: B 291 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: B 557 LEU cc_start: 0.9300 (mp) cc_final: 0.9095 (mm) REVERT: B 716 GLU cc_start: 0.8910 (tp30) cc_final: 0.8610 (tp30) REVERT: B 761 MET cc_start: 0.8453 (ppp) cc_final: 0.7928 (ppp) REVERT: B 769 GLU cc_start: 0.8769 (tp30) cc_final: 0.8453 (tp30) REVERT: B 773 ASN cc_start: 0.9298 (m-40) cc_final: 0.8742 (m-40) REVERT: B 807 TYR cc_start: 0.9406 (m-80) cc_final: 0.9145 (m-80) outliers start: 37 outliers final: 18 residues processed: 113 average time/residue: 0.4286 time to fit residues: 54.4810 Evaluate side-chains 97 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.090726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058578 restraints weight = 26501.511| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.54 r_work: 0.2707 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12990 Z= 0.314 Angle : 0.652 9.530 17678 Z= 0.329 Chirality : 0.047 0.206 2112 Planarity : 0.003 0.040 2182 Dihedral : 7.981 176.528 2254 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.94 % Favored : 93.79 % Rotamer: Outliers : 3.16 % Allowed : 24.40 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1498 helix: -3.42 (0.27), residues: 174 sheet: -1.76 (0.34), residues: 284 loop : 0.09 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 262 TYR 0.016 0.002 TYR A 751 PHE 0.030 0.002 PHE A 477 TRP 0.023 0.003 TRP A 796 HIS 0.007 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00733 (12946) covalent geometry : angle 0.64457 (17562) SS BOND : bond 0.00542 ( 16) SS BOND : angle 0.55970 ( 32) hydrogen bonds : bond 0.04882 ( 142) hydrogen bonds : angle 5.04897 ( 294) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.79430 ( 36) link_NAG-ASN : bond 0.00559 ( 16) link_NAG-ASN : angle 1.42411 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8632 (tp) cc_final: 0.8091 (pp) REVERT: A 197 LYS cc_start: 0.9205 (tppp) cc_final: 0.8944 (tppt) REVERT: A 291 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: A 716 GLU cc_start: 0.8886 (tp30) cc_final: 0.8568 (tp30) REVERT: A 761 MET cc_start: 0.8965 (pmm) cc_final: 0.8758 (pmm) REVERT: A 769 GLU cc_start: 0.8835 (tp30) cc_final: 0.8490 (tp30) REVERT: A 773 ASN cc_start: 0.9298 (m-40) cc_final: 0.8650 (m-40) REVERT: A 777 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6969 (tpp) REVERT: B 80 ILE cc_start: 0.8615 (tp) cc_final: 0.8061 (pp) REVERT: B 291 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: B 716 GLU cc_start: 0.8891 (tp30) cc_final: 0.8578 (tp30) REVERT: B 761 MET cc_start: 0.8508 (ppp) cc_final: 0.8033 (ppp) REVERT: B 769 GLU cc_start: 0.8824 (tp30) cc_final: 0.8532 (tp30) REVERT: B 773 ASN cc_start: 0.9347 (m-40) cc_final: 0.8814 (m-40) REVERT: B 777 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6953 (tpp) outliers start: 45 outliers final: 25 residues processed: 116 average time/residue: 0.4333 time to fit residues: 56.1179 Evaluate side-chains 101 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 241 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062216 restraints weight = 25948.921| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.46 r_work: 0.2779 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12990 Z= 0.104 Angle : 0.544 9.610 17678 Z= 0.275 Chirality : 0.042 0.182 2112 Planarity : 0.003 0.043 2182 Dihedral : 7.777 176.911 2254 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.07 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 25.39 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1498 helix: -3.33 (0.31), residues: 162 sheet: -1.74 (0.34), residues: 284 loop : 0.13 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.010 0.001 TYR B 233 PHE 0.027 0.002 PHE B 747 TRP 0.031 0.003 TRP A 793 HIS 0.003 0.000 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00242 (12946) covalent geometry : angle 0.54001 (17562) SS BOND : bond 0.00228 ( 16) SS BOND : angle 0.32972 ( 32) hydrogen bonds : bond 0.03502 ( 142) hydrogen bonds : angle 4.78250 ( 294) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.27155 ( 36) link_NAG-ASN : bond 0.00158 ( 16) link_NAG-ASN : angle 0.96403 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8599 (tp) cc_final: 0.8127 (pp) REVERT: A 197 LYS cc_start: 0.9209 (tppp) cc_final: 0.8935 (tppt) REVERT: A 716 GLU cc_start: 0.8850 (tp30) cc_final: 0.8527 (tp30) REVERT: A 761 MET cc_start: 0.8819 (pmm) cc_final: 0.8522 (pmm) REVERT: A 769 GLU cc_start: 0.8776 (tp30) cc_final: 0.8459 (tp30) REVERT: A 773 ASN cc_start: 0.9267 (m-40) cc_final: 0.8581 (m-40) REVERT: B 80 ILE cc_start: 0.8593 (tp) cc_final: 0.8100 (pp) REVERT: B 242 GLU cc_start: 0.9029 (pm20) cc_final: 0.8561 (pp20) REVERT: B 710 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8724 (mp10) REVERT: B 716 GLU cc_start: 0.8862 (tp30) cc_final: 0.8543 (tp30) REVERT: B 761 MET cc_start: 0.8543 (ppp) cc_final: 0.7974 (ppp) REVERT: B 769 GLU cc_start: 0.8806 (tp30) cc_final: 0.8483 (tp30) REVERT: B 773 ASN cc_start: 0.9311 (m-40) cc_final: 0.8726 (m-40) outliers start: 30 outliers final: 26 residues processed: 105 average time/residue: 0.4308 time to fit residues: 51.0861 Evaluate side-chains 101 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 298 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 298 HIS ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059999 restraints weight = 26102.073| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.49 r_work: 0.2718 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12990 Z= 0.242 Angle : 0.599 10.376 17678 Z= 0.304 Chirality : 0.045 0.170 2112 Planarity : 0.003 0.043 2182 Dihedral : 7.877 176.541 2254 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.87 % Favored : 93.86 % Rotamer: Outliers : 3.02 % Allowed : 24.26 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1498 helix: -3.36 (0.28), residues: 174 sheet: -1.77 (0.34), residues: 284 loop : 0.07 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.012 0.001 TYR A 751 PHE 0.037 0.002 PHE A 477 TRP 0.031 0.003 TRP A 796 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00569 (12946) covalent geometry : angle 0.59343 (17562) SS BOND : bond 0.00443 ( 16) SS BOND : angle 0.43507 ( 32) hydrogen bonds : bond 0.04307 ( 142) hydrogen bonds : angle 4.92861 ( 294) link_BETA1-4 : bond 0.00277 ( 12) link_BETA1-4 : angle 1.53427 ( 36) link_NAG-ASN : bond 0.00360 ( 16) link_NAG-ASN : angle 1.20852 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8592 (tp) cc_final: 0.8070 (pp) REVERT: A 197 LYS cc_start: 0.9239 (tppp) cc_final: 0.8964 (tppt) REVERT: A 291 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: A 673 MET cc_start: 0.9240 (mmt) cc_final: 0.8969 (mmt) REVERT: A 716 GLU cc_start: 0.8812 (tp30) cc_final: 0.8473 (tp30) REVERT: A 761 MET cc_start: 0.8880 (pmm) cc_final: 0.8634 (pmm) REVERT: A 769 GLU cc_start: 0.8830 (tp30) cc_final: 0.8540 (tp30) REVERT: A 773 ASN cc_start: 0.9255 (m-40) cc_final: 0.8590 (m-40) REVERT: B 80 ILE cc_start: 0.8570 (tp) cc_final: 0.8069 (pp) REVERT: B 242 GLU cc_start: 0.9031 (pm20) cc_final: 0.8609 (pp20) REVERT: B 291 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: B 671 ASP cc_start: 0.9498 (OUTLIER) cc_final: 0.9214 (m-30) REVERT: B 710 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: B 716 GLU cc_start: 0.8841 (tp30) cc_final: 0.8508 (tp30) REVERT: B 761 MET cc_start: 0.8501 (ppp) cc_final: 0.8037 (ppp) REVERT: B 769 GLU cc_start: 0.8862 (tp30) cc_final: 0.8501 (tp30) REVERT: B 773 ASN cc_start: 0.9328 (m-40) cc_final: 0.8764 (m-40) outliers start: 43 outliers final: 21 residues processed: 111 average time/residue: 0.4520 time to fit residues: 56.3163 Evaluate side-chains 95 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 73 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.094605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063139 restraints weight = 25887.323| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.44 r_work: 0.2790 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12990 Z= 0.096 Angle : 0.546 12.274 17678 Z= 0.276 Chirality : 0.042 0.222 2112 Planarity : 0.003 0.052 2182 Dihedral : 7.715 176.584 2254 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.34 % Favored : 94.39 % Rotamer: Outliers : 1.97 % Allowed : 25.25 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1498 helix: -3.03 (0.33), residues: 158 sheet: -1.73 (0.34), residues: 282 loop : 0.13 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.010 0.001 TYR B 185 PHE 0.029 0.001 PHE A 747 TRP 0.034 0.003 TRP A 796 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00220 (12946) covalent geometry : angle 0.54306 (17562) SS BOND : bond 0.00215 ( 16) SS BOND : angle 0.32822 ( 32) hydrogen bonds : bond 0.03336 ( 142) hydrogen bonds : angle 4.68320 ( 294) link_BETA1-4 : bond 0.00411 ( 12) link_BETA1-4 : angle 1.20916 ( 36) link_NAG-ASN : bond 0.00165 ( 16) link_NAG-ASN : angle 0.90397 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8618 (tp) cc_final: 0.8145 (pp) REVERT: A 197 LYS cc_start: 0.9245 (tppp) cc_final: 0.8966 (tppt) REVERT: A 291 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: A 671 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.9219 (m-30) REVERT: A 716 GLU cc_start: 0.8811 (tp30) cc_final: 0.8525 (tp30) REVERT: A 761 MET cc_start: 0.8753 (pmm) cc_final: 0.8480 (pmm) REVERT: A 769 GLU cc_start: 0.8854 (tp30) cc_final: 0.8480 (tp30) REVERT: A 773 ASN cc_start: 0.9228 (m-40) cc_final: 0.8532 (m-40) REVERT: A 807 TYR cc_start: 0.9417 (m-80) cc_final: 0.9088 (m-80) REVERT: B 80 ILE cc_start: 0.8596 (tp) cc_final: 0.8174 (pp) REVERT: B 242 GLU cc_start: 0.9009 (pm20) cc_final: 0.8554 (pp20) REVERT: B 291 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: B 710 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: B 716 GLU cc_start: 0.8828 (tp30) cc_final: 0.8538 (tp30) REVERT: B 761 MET cc_start: 0.8444 (ppp) cc_final: 0.8048 (ppp) REVERT: B 769 GLU cc_start: 0.8799 (tp30) cc_final: 0.8456 (tp30) REVERT: B 773 ASN cc_start: 0.9313 (m-40) cc_final: 0.8725 (m-40) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.4778 time to fit residues: 54.3392 Evaluate side-chains 97 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 298 HIS A 587 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 181 GLN B 298 HIS ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059722 restraints weight = 26453.782| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.34 r_work: 0.2736 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 12990 Z= 0.323 Angle : 0.669 10.899 17678 Z= 0.337 Chirality : 0.048 0.251 2112 Planarity : 0.003 0.049 2182 Dihedral : 8.028 176.797 2254 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.28 % Favored : 93.46 % Rotamer: Outliers : 2.25 % Allowed : 25.11 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1498 helix: -3.40 (0.28), residues: 174 sheet: -1.92 (0.33), residues: 284 loop : 0.04 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 121 TYR 0.016 0.002 TYR A 751 PHE 0.077 0.003 PHE B 794 TRP 0.039 0.004 TRP A 797 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00752 (12946) covalent geometry : angle 0.66226 (17562) SS BOND : bond 0.00556 ( 16) SS BOND : angle 0.56591 ( 32) hydrogen bonds : bond 0.04887 ( 142) hydrogen bonds : angle 5.14014 ( 294) link_BETA1-4 : bond 0.00287 ( 12) link_BETA1-4 : angle 1.73734 ( 36) link_NAG-ASN : bond 0.00575 ( 16) link_NAG-ASN : angle 1.44551 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8852 (tp) cc_final: 0.8640 (tm) REVERT: A 80 ILE cc_start: 0.8597 (tp) cc_final: 0.8098 (pp) REVERT: A 242 GLU cc_start: 0.8845 (pm20) cc_final: 0.8480 (pm20) REVERT: A 291 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: A 671 ASP cc_start: 0.9485 (OUTLIER) cc_final: 0.9221 (m-30) REVERT: A 716 GLU cc_start: 0.8756 (tp30) cc_final: 0.8431 (tp30) REVERT: A 761 MET cc_start: 0.8900 (pmm) cc_final: 0.8616 (pmm) REVERT: A 769 GLU cc_start: 0.8912 (tp30) cc_final: 0.8546 (tp30) REVERT: A 773 ASN cc_start: 0.9234 (m-40) cc_final: 0.8546 (m-40) REVERT: B 80 ILE cc_start: 0.8589 (tp) cc_final: 0.8080 (pp) REVERT: B 242 GLU cc_start: 0.9001 (pm20) cc_final: 0.8623 (pp20) REVERT: B 291 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8650 (mp0) REVERT: B 673 MET cc_start: 0.9247 (mmt) cc_final: 0.8980 (mmt) REVERT: B 710 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8769 (mp10) REVERT: B 716 GLU cc_start: 0.8783 (tp30) cc_final: 0.8480 (tp30) REVERT: B 769 GLU cc_start: 0.8876 (tp30) cc_final: 0.8490 (tp30) REVERT: B 773 ASN cc_start: 0.9352 (m-40) cc_final: 0.8695 (m-40) outliers start: 32 outliers final: 22 residues processed: 102 average time/residue: 0.4128 time to fit residues: 47.4938 Evaluate side-chains 95 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.093237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061924 restraints weight = 26280.647| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.36 r_work: 0.2768 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12990 Z= 0.141 Angle : 0.573 12.147 17678 Z= 0.291 Chirality : 0.044 0.241 2112 Planarity : 0.003 0.050 2182 Dihedral : 7.898 177.185 2254 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.47 % Favored : 94.26 % Rotamer: Outliers : 1.69 % Allowed : 25.95 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1498 helix: -3.26 (0.30), residues: 174 sheet: -1.92 (0.33), residues: 284 loop : 0.02 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.010 0.001 TYR B 233 PHE 0.078 0.002 PHE B 794 TRP 0.049 0.004 TRP B 797 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00338 (12946) covalent geometry : angle 0.56879 (17562) SS BOND : bond 0.00288 ( 16) SS BOND : angle 0.36860 ( 32) hydrogen bonds : bond 0.03726 ( 142) hydrogen bonds : angle 4.94643 ( 294) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 1.32712 ( 36) link_NAG-ASN : bond 0.00135 ( 16) link_NAG-ASN : angle 1.05295 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3467.69 seconds wall clock time: 59 minutes 57.79 seconds (3597.79 seconds total)